HEADER HYDROLASE 20-JUL-09 3ID3 TITLE CRYSTAL STRUCTURE OF RSEP PDZ2 I304A DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF SIGMA E PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PDZ2 DOMAIN, RESIDUES 222-309; COMPND 5 EC: 3.4.24.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: RSEP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HYDROLASE, CELL INNER MEMBRANE, CELL MEMBRANE, MEMBRANE, METAL- KEYWDS 2 BINDING, METALLOPROTEASE, PROTEASE, TRANSMEMBRANE, ZINC EXPDTA X-RAY DIFFRACTION AUTHOR X.LI,B.WANG,L.FENG,J.WANG,Y.SHI REVDAT 4 01-NOV-23 3ID3 1 REMARK REVDAT 3 10-NOV-21 3ID3 1 SEQADV REVDAT 2 08-SEP-09 3ID3 1 JRNL REVDAT 1 11-AUG-09 3ID3 0 JRNL AUTH X.LI,B.WANG,L.FENG,H.KANG,Y.QI,J.WANG,Y.SHI JRNL TITL CLEAVAGE OF RSEA BY RSEP REQUIRES A CARBOXYL-TERMINAL JRNL TITL 2 HYDROPHOBIC AMINO ACID FOLLOWING DEGS CLEAVAGE JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 14837 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19706448 JRNL DOI 10.1073/PNAS.0903289106 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.4 REMARK 3 NUMBER OF REFLECTIONS : 9988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 491 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.9987 - 3.1911 0.89 2573 164 0.1776 0.1969 REMARK 3 2 3.1911 - 2.5329 0.93 2687 150 0.2037 0.2535 REMARK 3 3 2.5329 - 2.2127 0.93 2697 96 0.2079 0.2277 REMARK 3 4 2.2127 - 2.0104 0.54 1540 81 0.2046 0.2130 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 41.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.64400 REMARK 3 B22 (A**2) : -7.08000 REMARK 3 B33 (A**2) : 1.98000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1344 REMARK 3 ANGLE : 0.936 1824 REMARK 3 CHIRALITY : 0.061 214 REMARK 3 PLANARITY : 0.005 240 REMARK 3 DIHEDRAL : 17.633 516 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 1.5992 -2.7351 -9.1415 REMARK 3 T TENSOR REMARK 3 T11: 0.2117 T22: 0.1465 REMARK 3 T33: 0.0011 T12: 0.0112 REMARK 3 T13: 0.0616 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.3052 L22: 0.5562 REMARK 3 L33: 0.3240 L12: 0.3269 REMARK 3 L13: 0.2642 L23: 0.5245 REMARK 3 S TENSOR REMARK 3 S11: 0.0383 S12: -0.0009 S13: -0.0425 REMARK 3 S21: 0.0410 S22: -0.0818 S23: 0.0372 REMARK 3 S31: 0.0021 S32: -0.0092 S33: 0.0197 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -8.8450 -11.8635 -23.5445 REMARK 3 T TENSOR REMARK 3 T11: 0.2012 T22: 0.1502 REMARK 3 T33: 0.0456 T12: 0.0223 REMARK 3 T13: 0.0427 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.6647 L22: 0.3404 REMARK 3 L33: 0.3695 L12: 0.6868 REMARK 3 L13: 0.1266 L23: 0.3408 REMARK 3 S TENSOR REMARK 3 S11: 0.0523 S12: 0.0000 S13: 0.0499 REMARK 3 S21: -0.0295 S22: 0.0162 S23: 0.0087 REMARK 3 S31: -0.0288 S32: 0.0384 S33: 0.0052 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 0:88 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 0:88 ) REMARK 3 ATOM PAIRS NUMBER : 661 REMARK 3 RMSD : 0.032 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ID3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR-H REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 49.983 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : 1.550 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 9.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 0.61 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33500 REMARK 200 FOR SHELL : 3.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2ZPM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.07350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LYS B 292 O HOH B 325 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ID1 RELATED DB: PDB REMARK 900 RSEP PDZ1 DOMAIN REMARK 900 RELATED ID: 3ID2 RELATED DB: PDB REMARK 900 RSEP PDZ2 DOMAIN REMARK 900 RELATED ID: 3ID4 RELATED DB: PDB REMARK 900 RSEP PDZ2 FUSED GKASPV PEPTIDE DOMAIN DBREF 3ID3 A 222 309 UNP P0AEH1 RSEP_ECOLI 222 309 DBREF 3ID3 B 222 309 UNP P0AEH1 RSEP_ECOLI 222 309 SEQADV 3ID3 MET A 221 UNP P0AEH1 EXPRESSION TAG SEQADV 3ID3 ALA A 304 UNP P0AEH1 ILE 304 ENGINEERED MUTATION SEQADV 3ID3 MET B 221 UNP P0AEH1 EXPRESSION TAG SEQADV 3ID3 ALA B 304 UNP P0AEH1 ILE 304 ENGINEERED MUTATION SEQRES 1 A 89 MET ILE GLU PRO VAL LEU GLU ASN VAL GLN PRO ASN SER SEQRES 2 A 89 ALA ALA SER LYS ALA GLY LEU GLN ALA GLY ASP ARG ILE SEQRES 3 A 89 VAL LYS VAL ASP GLY GLN PRO LEU THR GLN TRP VAL THR SEQRES 4 A 89 PHE VAL MET LEU VAL ARG ASP ASN PRO GLY LYS SER LEU SEQRES 5 A 89 ALA LEU GLU ILE GLU ARG GLN GLY SER PRO LEU SER LEU SEQRES 6 A 89 THR LEU ILE PRO GLU SER LYS PRO GLY ASN GLY LYS ALA SEQRES 7 A 89 ILE GLY PHE VAL GLY ALA GLU PRO LYS VAL ILE SEQRES 1 B 89 MET ILE GLU PRO VAL LEU GLU ASN VAL GLN PRO ASN SER SEQRES 2 B 89 ALA ALA SER LYS ALA GLY LEU GLN ALA GLY ASP ARG ILE SEQRES 3 B 89 VAL LYS VAL ASP GLY GLN PRO LEU THR GLN TRP VAL THR SEQRES 4 B 89 PHE VAL MET LEU VAL ARG ASP ASN PRO GLY LYS SER LEU SEQRES 5 B 89 ALA LEU GLU ILE GLU ARG GLN GLY SER PRO LEU SER LEU SEQRES 6 B 89 THR LEU ILE PRO GLU SER LYS PRO GLY ASN GLY LYS ALA SEQRES 7 B 89 ILE GLY PHE VAL GLY ALA GLU PRO LYS VAL ILE FORMUL 3 HOH *141(H2 O) HELIX 1 1 SER A 233 GLY A 239 1 7 HELIX 2 2 GLN A 256 ASN A 267 1 12 HELIX 3 3 SER B 233 GLY B 239 1 7 HELIX 4 4 GLN B 256 ASN B 267 1 12 SHEET 1 A 2 LEU A 226 VAL A 229 0 SHEET 2 A 2 ALA A 304 PRO A 306 -1 O GLU A 305 N GLU A 227 SHEET 1 B 4 GLN A 252 PRO A 253 0 SHEET 2 B 4 ARG A 245 VAL A 249 -1 N VAL A 249 O GLN A 252 SHEET 3 B 4 LEU A 272 ARG A 278 -1 O GLU A 277 N ARG A 245 SHEET 4 B 4 SER A 281 LEU A 287 -1 O LEU A 285 N LEU A 274 SHEET 1 C 2 LEU B 226 VAL B 229 0 SHEET 2 C 2 ALA B 304 PRO B 306 -1 O GLU B 305 N GLU B 227 SHEET 1 D 4 GLN B 252 PRO B 253 0 SHEET 2 D 4 ARG B 245 VAL B 249 -1 N VAL B 249 O GLN B 252 SHEET 3 D 4 LEU B 272 ARG B 278 -1 O GLU B 277 N ARG B 245 SHEET 4 D 4 SER B 281 LEU B 287 -1 O LEU B 285 N LEU B 274 CRYST1 47.411 38.147 51.265 90.00 102.84 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021092 0.000000 0.004807 0.00000 SCALE2 0.000000 0.026214 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020007 0.00000